Mr Salmond, the party's Westminster group leader, told the SNP's autumn conference in Dundee that there should be a measured response by the West to the attacks.
Islamic extremist Osama Bin Laden has been named by the US as the prime suspect for the attacks.
However, there have been reports of a backlash against people in the Asian community in Britain.
Muslim leaders in Scotland say members of their community have been harassed and there have been reports of telephone threats to the central mosque in Glasgow.
But there was one dissenting voice at the delegation, who labelled the conference resolution "politically correct claptrap".
Nevertheless, the resolution that called on parliament to extend racial hatred legislation to cover colour, religion, nationality, ethnic origin or sexual orientation, was carried by a huge majority.
Mr Salmond told delegates: "This is not a war against Islam.
"The Islamic faith is one of the world's great religions."
Earlier, Mr Salmond had put the finishing touches to his conference speech with the help of party delegate, Jahangir Hanif.
The former SNP leader referred to the words of US President George W Bush, who said attacks on Muslims represented not the best of America, but the worst of humanity.
Mr Salmond said: "We are privileged to have in Scotland one of the most productive and patriotic Muslim communities.
"They are far more part of Scottish society than the morons and thugs who have been threatening them will ever be."
'Democracy and decency'
In a speech to the conference on Wednesday, Pakistan-born Muslim and prominent SNP member, Bashir Ahmed, said: "I know there are some few in our society who will see what has happened as an excuse to attack those who seem different.
"But I stand today, as do all Scottish Muslims, alongside our fellow Scots, united in a determination that democracy and decency will prevail."
Mr Salmond echoed the calls of party leader John Swinney for caution in response to the attacks, as hostilities between the United States and Afghanistan, which is reported to be in hiding, intensify.
Mr Swinney said there must be clear evidence against those targeted by the US and its allies and that action must be based on bringing those people to justice.
Mr Salmond, the MP for Banff and Buchan, called for the response to be "proportionate, reasoned and effective".
He said: "We must attack the cause, as well as the symptoms, of terror."
Mr Hanif said: "We are all Scots and we should try and be united to find these extremists but we cannot do it if we are divided amongst ourselves.
"If we are fighting each other than how can we go and hunt our common enemy - these extremists want us to be divided."
Dissenting voice
Party activist Andrew Leslie, from West Lothian, said the call for more legislation was no more than a "touchy feely" sentiment, lacking intellectual rigour.
He said: "Most of this resolution is anodyne politically-correct claptrap that does nothing whatsoever to advance us towards independence.
"You don't legislate hatred out of existence, you get rid of hatred, difficult though it is, by creating the conditions where there is no need for it to grow."
But another delegate, Andrew Doig, rejected Mr Leslie's argument.
Mr Doig said: "This is not an anodyne motion but about the issues that affect real people in Scotland today."